DOCSLIB.ORG

Structure of the Activated Edc1-Dcp1-Dcp2-Edc3 Mrna Decapping Complex with Substrate Analog Poised for Catalysis

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Structure of the Activated Edc1-Dcp1-Dcp2-Edc3 Mrna Decapping Complex with Substrate Analog Poised for Catalysis ARTICLE DOI: 10.1038/s41467-018-03536-x OPEN Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis Jeffrey S. Mugridge1, Ryan W. Tibble1,2, Marcin Ziemniak3,4,5, Jacek Jemielity4 & John D. Gross 1,2 The conserved decapping enzyme Dcp2 recognizes and removes the 5′ eukaryotic cap from mRNA transcripts in a critical step of many cellular RNA decay pathways. Dcp2 is a dynamic 1234567890():,; enzyme that functions in concert with the essential activator Dcp1 and a diverse set of coactivators to selectively and efficiently decap target mRNAs in the cell. Here we present a 2.84 Å crystal structure of K. lactis Dcp1–Dcp2 in complex with coactivators Edc1 and Edc3, and with substrate analog bound to the Dcp2 active site. Our structure shows how Dcp2 recognizes cap substrate in the catalytically active conformation of the enzyme, and how coactivator Edc1 forms a three-way interface that bridges the domains of Dcp2 to consolidate the active conformation. Kinetic data reveal Dcp2 has selectivity for the first transcribed nucleotide during the catalytic step. The heterotetrameric Edc1–Dcp1–Dcp2–Edc3 structure shows how coactivators Edc1 and Edc3 can act simultaneously to activate decapping catalysis. 1 Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA. 2 Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA 94158, USA. 3 Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland. 4 Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland. 5Present address: Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089 Warsaw, Poland. Correspondence and requests for materials should be addressed to J.D.G. (email: [email protected]) NATURE COMMUNICATIONS | (2018) 9:1152 | DOI: 10.1038/s41467-018-03536-x | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-03536-x egradation of mRNA transcripts plays a critical role in Dcp2 NRD as in our Mugridge et al. substrate-bound structure, maintenance of the cellular transcriptome and in control but the CD was rotated by ~90° to bring the Nudix helix much D 1 7 7 of eukaryotic gene expression . Removal of the m GpppN closer to the cleaved m GDP product, consistent with an active cap structure found at the 5′ end of all eukaryotic mRNA marks conformation of Dcp222. Finally, most recently Wurm et al. these transcripts for rapid clearance via the 5′-to-3′ mRNA decay published a study that presented an S. pombe Edc1–Dcp1–Dcp2 pathway2. The conserved mRNA-decapping enzyme Dcp2 cata- product-bound structure in the same conformation as observed lyzes hydrolysis of the 5′ cap to liberate m7GDP and 5′ mono- by Charenton et al., a conformation that is significantly populated phosphate RNA, which can then be degraded by conserved 5′-3′ in solution when Edc1 and m7GDP or capped RNA are bound19. – exonucleases3 6. Dcp2-mediated decapping is a critical step in In this study, we present a new, four-protein structure of K. many cellular RNA decay pathways including bulk 5′–3′ decay4,5, lactis Edc1–Dcp1–Dcp2–Edc3 at 2.84 Å resolution in the cataly- – nonsense-mediated decay7 10, microRNA-mediated decay11,12, tically active conformation with bound substrate analog poised decay of long-noncoding RNA13, and decay of transcripts con- for catalysis. We show that the conserved YAGxxF activation taining non-optimal codons14. Recently, Dcp2 was also shown to motif of Edc1 mediates a three-way interface between Dcp1 and be a reader of reversible m6A modifications in the 5′ cap, whereby the Dcp2 NRD and CD, and that lesions on the NRD and in the m6A methylation inhibits decapping and stabilizes cellular flexible hinge linking the CD and NRD abolish activation by mRNA transcripts15. Edc1. Substrate analog binding to the active conformation of Dcp2 consists of an N-terminal regulatory domain (NRD) and Dcp2 suggests that the first transcribed nucleotide of RNA is a catalytic Nudix domain (CD)16,17 linked by a short, flexible recognized by base stacking to a conserved aromatic residue at the hinge that allows the enzyme to dynamically adopt different top of the RNA-binding channel, and that the RNA body follows – conformations in solution18,19 and in crystal structures20 24. The this positively charged path to bound Edc3 coactivator. We show CD harbors a positively charged patch for RNA binding (box B that Dcp2 has selectivity for the first transcribed nucleotide of motif)25,26 and a Nudix motif with conserved Glu residues that RNA substrate and that this selectivity depends on the conserved bind magnesium and carry out cap hydrolysis chemistry27,28. aromatic residue that binds this nucleotide of our substrate Fungal Dcp2 also contains an unstructured C-terminal extension analog. Overall, these data show how substrate binds and is that harbors protein–protein interaction motifs and elements that recognized by the catalytically active conformation of Dcp2, inhibit Dcp2 catalysis29. At least some of these motifs are trans- suggest a path for RNA binding consistent with prior in vitro ferred to the C-terminus of the essential activator Dcp1 in mutagenesis and binding data, and show how coactivators Edc1 metazoans, suggesting a conserved biological function30. The and Edc3 can simultaneously bind Dcp2 to enhance mRNA NRD enhances decapping activity by specifically recognizing the decapping by the Dcp1–Dcp2 complex. Our structure establishes m7G nucleotide of cap and binding Dcp1, which further accel- that the active conformation of Dcp2 is the same for both sub- erates decapping17,19,21,22,31,32. strate and product-bound complexes, and clarifies the mechan- The activity of the core Dcp1–Dcp2 complex can be further isms of decapping catalysis and control of decapping activation by modulated by the enhancer of decapping proteins (Edcs)33. For multiple protein interactions. example, the Edc1-type activators, which include the yeast paralog Edc2 and PNRC2 in metazoans, contain conserved tan- dem short linear motifs to bind Dcp1 and activate Dcp2 cata- Results – – lysis19 21,34 37. Edc3 activates decapping by promoting RNA Structure of substrate analog-bound Edc1–Dcp1–Dcp2–Edc3. – binding and alleviating autoinhibition of Dcp2 in yeast22,29,38 42. To obtain our recently published substrate analog-bound Edc3 is recruited to the decapping complex via short linear motifs PNRC2–Dcp1–Dcp2 structure21, we crystallized an apo found in the fungal or metazoan Dcp2 or Dcp1 C-terminal PNRC2–Dcp1–Dcp2 complex and soaked in cap analog to induce extension, respectively29,33. Edc4 is a metazoan-specific scaf- a conformational change and substrate binding within the crystal. folding protein that strengthens Dcp1–Dcp2 interaction and While this substrate-bound conformation gave new insight into coordinates decapping with exonucleolytic degradation by cap recognition by Dcp2, it was clear that this did not represent – Xrn132,43 45. Genetic and physical interactions between activator the catalytically active conformation because the catalytic Glu proteins suggest these cofactors work together to promote dec- residue on the Nudix helix was positioned to too far from bound apping, but how this is achieved at the structural level is substrate to carry out hydrolysis chemistry. When we attempted – unknown45 49. to push Dcp2 into the active conformation by soaking in cata- Several recent structural studies have provided new insights lytically required magnesium along with substrate analog, the into how Dcp2 recognizes the m7G cap, how Dcp2 activity is crystals were physically damaged and diffraction was completely enhanced by coactivators, and how Dcp2 solution conformations destroyed, suggesting this induced an additional conformational are tied to catalysis. First, a study by Valkov et al. presented a change in Dcp2 that could not be accommodated by the crystal structure of S. pombe Edc1–Dcp1–Dcp2 in which the activation lattice. motif in Edc1 bridges the Dcp2 NRD and CD to apparently To trap the substrate-bound active conformation, we screened promote a conformation of Dcp2 that enhances RNA binding20. different Dcp1–Dcp2 constructs (S. pombe, K. lactis, H. sapiens) Soon after, our lab published the first substrate analog-bound in which the catalytic Glu was mutated to Gln to prevent cap structure of S. pombe Dcp1–Dcp2 in complex with human hydrolysis for co-crystallization with magnesium, a tight-binding PNRC221. Our structure showed a very different conformation two-headed cap analog50, and coactivators Edc1 and Edc3 than the Valkov structure, in which the substrate analog was (Fig. 1a,b). The K. lactis constructs crystallized most readily and bound by a composite binding site using conserved residues on we obtained a structure of Kl Edc1–Dcp1–Dcp2–Edc3 with the NRD and CD. However, in this pre-catalytic conformation of bound magnesium and two-headed cap analog at 2.84 Å Dcp2 the catalytic Glu on the Nudix helix was positioned too far resolution (Fig. 1c, Table 1, solved by molecular replacement from substrate for effective catalysis, and the activation motif of with PDB 5LOP22 Dcp1–Dcp2). Dcp2 is in the catalytically active PNRC2 was disordered, suggesting an additional conformational conformation, very similar to that found in recently reported change in Dcp2 was needed to achieve catalysis. Simultaneously, m7GDP product-bound structures (Supplementary
Load more

Recommended publications
  • Integrative Analysis of Phenomic, Genomic, and Transcriptomic To
    bioRxiv preprint doi: https://doi.org/10.1101/2020.11.29.392167; this version posted November 30, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Integrative Analysis of Phenomic, Genomic, and Transcriptomic to Identify Potential Functional Genes of Yaks in Plain and Plateau Jiabo Wang1,2, §, Jiuqiang Guan3, §, Kangzhu Yixi1,2,Tao Shu1, Zhixin Chai1,2, Jikun Wang1,2, Hui Wang1,2, Zhijuan Wu1,2, Xin Cai1,2, Jincheng Zhong1,2*,Xiaolin Luo3* 1. Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education，Chengdu, Sichuan, China; 2. Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Chengdu, Sichuan, China; 3. Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China; §These authors contributed equally to this work. *Correspondences should be addressed to JZ ([email protected]) and XL ([email protected]) bioRxiv preprint doi: https://doi.org/10.1101/2020.11.29.392167; this version posted November 30, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Background: The yak is an important source of livelihood for the people living in the Qinghai-Tibet Plateau. Most genetics detection studies have focused on the comparison between different tissues of different breeds, both living in the Plateau and in the plains. The genetic background and complex regulatory relationship have frequently puzzled researchers. In this study, we divided a population of 10 yaks into two subgroups, namely Plateau (living in the Plateau) and Plain (living in the plains).
    [Show full text]
  • IP6K1 Upregulates the Formation of Processing Bodies by Promoting Proteome Remodeling on the Mrna Cap
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.13.199828; this version posted July 13, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. IP6K1 upregulates the formation of processing bodies by promoting proteome remodeling on the mRNA cap Akruti Shah1,2 and Rashna Bhandari1* 1Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics (CDFD), Inner Ring Road, Uppal, Hyderabad 500039, India. 2Graduate studies, Manipal Academy of Higher Education, Manipal 576104, India. *Correspondence to Rashna Bhandari; Email: [email protected] Running title: IP6K1 promotes mRNA turnover to induce P-bodies ORCID IDs Akruti Shah - 0000-0001-9557-4952 Rashna Bhandari - 0000-0003-3101-0204 This PDF file includes: Main Text Figures 1 to 6 Keywords mRNA decay/mRNA metabolism/P-bodies/translation suppression 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.13.199828; this version posted July 13, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Inositol hexakisphosphate kinases (IP6Ks) are ubiquitously expressed small molecule kinases that catalyze the conversion of the inositol phosphate IP6 to 5-IP7. IP6Ks have been reported to influence cellular functions by protein-protein interactions independent of their enzymatic activity.
    [Show full text]
  • Mutations in DCPS and EDC3 in Autosomal Recessive Intellectual
    Human Molecular Genetics, 2015, Vol. 24, No. 11 3172–3180 doi: 10.1093/hmg/ddv069 Advance Access Publication Date: 20 February 2015 Original Article Downloaded from ORIGINAL ARTICLE Mutations in DCPS and EDC3 in autosomal recessive intellectual disability indicate a crucial role for mRNA http://hmg.oxfordjournals.org/ decapping in neurodevelopment Iltaf Ahmed1,2,†, Rebecca Buchert3,†, Mi Zhou5,†, Xinfu Jiao5,†, Kirti Mittal1, Taimoor I. Sheikh1, Ute Scheller3, Nasim Vasli1, Muhammad Arshad Rafiq1, 6 1 7 2 M. Qasim Brohi , Anna Mikhailov , Muhammad Ayaz , Attya Bhatti , at Universitaet Erlangen-Nuernberg, Wirtschafts- und Sozialwissenschaftliche Z on August 15, 2016 Heinrich Sticht4, Tanveer Nasr8,9, Melissa T. Carter10, Steffen Uebe3, André Reis3, Muhammad Ayub7,11, Peter John2, Megerditch Kiledjian5,*, John B. Vincent1,12,13,* and Rami Abou Jamra3,* 1Molecular Neuropsychiatry and Development Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario, Canada M5T 1R8, 2Atta-ur-Rehman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan, 3Institute of Human Genetics and 4Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany, 5Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA, 6Sir Cowasji Jehangir Institute of Psychiatry, Hyderabad, Sindh 71000, Pakistan, 7Lahore Institute of Research and Development,
    [Show full text]
  • Role of DCP1-DCP2 Complex Regulated by Viral and Host Micrornas in DNA Virus Infection T
    Fish and Shellfish Immunology 92 (2019) 21–30 Contents lists available at ScienceDirect Fish and Shellfish Immunology journal homepage: www.elsevier.com/locate/fsi Full length article Role of DCP1-DCP2 complex regulated by viral and host microRNAs in DNA virus infection T ∗ Yuechao Sun, Xiaobo Zhang College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou, 310058, People's Republic of China ARTICLE INFO ABSTRACT Keywords: The DCP1-DCP2 complex can regulate the antiviral immunity of animals by the decapping of retrovirus RNAs DCP1-DCP2 complex and the suppression of RNAi during RNA virus infection. However, the influence of DCP1-DCP2 complex on DNA miRNA virus infection and the regulation of DCP1-DCP2 complex by microRNAs (miRNAs) remain unclear. In this study, DNA virus infection the role of miRNA-regulated DCP1-DCP2 complex in DNA virus infection was characterized. Our results showed that the DCP1-DCP2 complex played a positive role in the infection of white spot syndrome virus (WSSV), a DNA virus of shrimp. In the DCP1-DCP2 complex, the N-terminal regulatory domain of DCP2 was interacted with the EVH1 domain of DCP1. Furthermore, shrimp miRNA miR-87 inhibited WSSV infection by targeting the host DCP2 gene and viral miRNA WSSV-miR-N46 took a negative effect on WSSV replication by targeting the host DCP1 gene. Therefore, our study provided novel insights into the underlying mechanism of DCP1-DCP2 complex and its regulation by miRNAs in virus-host interactions. Importance: During RNA virus infection, the DCP1-DCP2 complex can play important roles in the animal anti- viral immunity by decapping retrovirus RNAs and suppressing RNAi.
    [Show full text]
  • Atxn2-CAG100-Knockin Mouse Spinal Cord Shows Progressive TDP43
    bioRxiv preprint doi: https://doi.org/10.1101/838177; this version posted November 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Atxn2-CAG100-KnockIn mouse spinal cord shows progressive TDP43 pathology associated with cholesterol biosynthesis suppression Júlia Canet-Pons1§, Nesli-Ece Sen1,2§, Aleksandar Arsovic1, Luis-Enrique Almaguer-Mederos1,3, Melanie V. Halbach1, Jana Key1,2, Claudia Döring4, Anja Kerksiek5, Gina Picchiarelli6, Raphaelle Cassel6, Frédérique René6, Stéphane Dieterlé6, Nina Hein-Fuchs7, Renate König7, Luc Dupuis6, Dieter Lütjohann5, Suzana Gispert1, Georg Auburger1# 1 Experimental Neurology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany; 2 Faculty of Biosciences, Goethe University, 60438 Frankfurt am Main, Germany; 3 Center for Investigation and Rehabilitation of Hereditary Ataxias (CIRAH), Holguín, Cuba; 4 Dr. Senckenberg Institute of Pathology, Medical Faculty, Goethe University, 60590 Frankfurt am Main, Germany; 5 Institute for Clinical Chemistry and Clinical Pharmacology, Medical Faculty, University Bonn, 53127 Bonn, Nordrhein-Westfalen, Germany; 6 UMRS-1118 INSERM, Faculty of Medicine, University of Strasbourg, 67000 Strasbourg, France; 7 Host-Pathogen Interactions, Paul-Ehrlich-Institute, 63225 Langen, Germany. § Joint first authorship # Correspondence to: [email protected], Tel: +49-69-6301-7428, FAX: +49-69-6301-7142 Acknowledgements: 1 bioRxiv preprint doi: https://doi.org/10.1101/838177; this version posted November 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • 4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).
    [Show full text]
  • 1 AGING Supplementary Table 2
    SUPPLEMENTARY TABLES Supplementary Table 1. Details of the eight domain chains of KIAA0101. Serial IDENTITY MAX IN COMP- INTERFACE ID POSITION RESOLUTION EXPERIMENT TYPE number START STOP SCORE IDENTITY LEX WITH CAVITY A 4D2G_D 52 - 69 52 69 100 100 2.65 Å PCNA X-RAY DIFFRACTION √ B 4D2G_E 52 - 69 52 69 100 100 2.65 Å PCNA X-RAY DIFFRACTION √ C 6EHT_D 52 - 71 52 71 100 100 3.2Å PCNA X-RAY DIFFRACTION √ D 6EHT_E 52 - 71 52 71 100 100 3.2Å PCNA X-RAY DIFFRACTION √ E 6GWS_D 41-72 41 72 100 100 3.2Å PCNA X-RAY DIFFRACTION √ F 6GWS_E 41-72 41 72 100 100 2.9Å PCNA X-RAY DIFFRACTION √ G 6GWS_F 41-72 41 72 100 100 2.9Å PCNA X-RAY DIFFRACTION √ H 6IIW_B 2-11 2 11 100 100 1.699Å UHRF1 X-RAY DIFFRACTION √ www.aging-us.com 1 AGING Supplementary Table 2. Significantly enriched gene ontology (GO) annotations (cellular components) of KIAA0101 in lung adenocarcinoma (LinkedOmics). Leading Description FDR Leading Edge Gene EdgeNum RAD51, SPC25, CCNB1, BIRC5, NCAPG, ZWINT, MAD2L1, SKA3, NUF2, BUB1B, CENPA, SKA1, AURKB, NEK2, CENPW, HJURP, NDC80, CDCA5, NCAPH, BUB1, ZWILCH, CENPK, KIF2C, AURKA, CENPN, TOP2A, CENPM, PLK1, ERCC6L, CDT1, CHEK1, SPAG5, CENPH, condensed 66 0 SPC24, NUP37, BLM, CENPE, BUB3, CDK2, FANCD2, CENPO, CENPF, BRCA1, DSN1, chromosome MKI67, NCAPG2, H2AFX, HMGB2, SUV39H1, CBX3, TUBG1, KNTC1, PPP1CC, SMC2, BANF1, NCAPD2, SKA2, NUP107, BRCA2, NUP85, ITGB3BP, SYCE2, TOPBP1, DMC1, SMC4, INCENP. RAD51, OIP5, CDK1, SPC25, CCNB1, BIRC5, NCAPG, ZWINT, MAD2L1, SKA3, NUF2, BUB1B, CENPA, SKA1, AURKB, NEK2, ESCO2, CENPW, HJURP, TTK, NDC80, CDCA5, BUB1, ZWILCH, CENPK, KIF2C, AURKA, DSCC1, CENPN, CDCA8, CENPM, PLK1, MCM6, ERCC6L, CDT1, HELLS, CHEK1, SPAG5, CENPH, PCNA, SPC24, CENPI, NUP37, FEN1, chromosomal 94 0 CENPL, BLM, KIF18A, CENPE, MCM4, BUB3, SUV39H2, MCM2, CDK2, PIF1, DNA2, region CENPO, CENPF, CHEK2, DSN1, H2AFX, MCM7, SUV39H1, MTBP, CBX3, RECQL4, KNTC1, PPP1CC, CENPP, CENPQ, PTGES3, NCAPD2, DYNLL1, SKA2, HAT1, NUP107, MCM5, MCM3, MSH2, BRCA2, NUP85, SSB, ITGB3BP, DMC1, INCENP, THOC3, XPO1, APEX1, XRCC5, KIF22, DCLRE1A, SEH1L, XRCC3, NSMCE2, RAD21.
    [Show full text]
  • Epigenetic Loss of the RNA Decapping Enzyme NUDT16 Mediates C-MYC Activation in T-Cell Acute Lymphoblastic Leukemia
    OPEN Leukemia (2017) 31, 1622–1657 www.nature.com/leu LETTERS TO THE EDITOR Epigenetic loss of the RNA decapping enzyme NUDT16 mediates C-MYC activation in T-cell acute lymphoblastic leukemia Leukemia (2017) 31, 1622–1625; doi:10.1038/leu.2017.99 Having found the aforementioned NUDT16 CpG island methy- lation profiles, we studied in greater detail their association with the possible transcriptional inactivation of the NUDT16 gene at the RNA and protein levels in leukemia cell lines. We first It is possible that the occurrence of intrinsic defects in RNA performed bisulfite genomic sequencing of mutiple clones in the – processing pathways, such as RNA decapping,1 3 contribute to the T-cell Acute Lymphoblastic Leukemia (T-ALL) cell lines CCRF-CEM, distorted RNA landscapes of cancer cells. After transcription by Jurkat, MOLT-4 and MOLT-16 using primers that encompassed the RNA polymerase II, RNA molecules are equipped with a 5´-end transcription start site-associated CpG island and confirmed the N7-methyl guanosine (m7G)-cap. This m7G-cap is essential for hypermethylated status of the 5′-end region of NUDT16 in translation, stabilizing the RNA molecule and protecting it from comparison to normal T lymphocytes (Figure 1b), validating the – exonucleolytic breakdown.1 3 For RNA decay to occur the DNA methylation patterns obtained by the microarray approach m7G-cap first needs to be removed. This process is known as (Supplementary Figure S2). In contrast, normal T lymphocytes, the – decapping.1 3 The decapping mRNA 2 (DCP2) enzyme,4 also T-ALL cell lines KOPN-8, REH and RS4;11 and the leukemia cell known as the nucleoside diphosphate-linked moiety X motif lines HL-60 and K562 derived from myeloid lineage were all found 20 (NUDT20), was originally thought to be the only mammalian to be unmethylated (Figure 1b; Supplementary Figure S2).
    [Show full text]
  • Uttrykking Final Ph[1].D THESIS TUYEN 27.10.06
    Nuclear Receptor Coregulators Role of Protein-Protein Interactions and cAMP/PKA Signaling Tuyen Thi Van Hoang Dissertation for the degree philosophiae doctor (PhD) at the University of Bergen October 2006 2 TABLE OF CONTENTS SCIENTIFIC ENVIRONMENTS.............................................................................................. 5 ACKNOWLEDGEMENTS ....................................................................................................... 7 LIST OF PAPERS...................................................................................................................... 9 ABBREVIATIONS.................................................................................................................. 11 PREFACE ................................................................................................................................ 13 INTRODUCTION.................................................................................................................... 15 1. Nuclear receptors ........................................................................................................... 15 1.1. Functional and structural domains ............................................................................ 15 1.2. Subfamilies and activation mechanisms ................................................................... 15 1.3. Steroidogenic factor-1............................................................................................... 19 1.3.1. Functional and structural domains ....................................................................
    [Show full text]
  • Chain Gene Induced by GM-CSF Β Receptor Regulation of Human High-Affinity Ige Molecular Mechanisms for Transcriptional
    Molecular Mechanisms for Transcriptional Regulation of Human High-Affinity IgE Receptor β-Chain Gene Induced by GM-CSF This information is current as Kyoko Takahashi, Natsuko Hayashi, Shuichi Kaminogawa of September 23, 2021. and Chisei Ra J Immunol 2006; 177:4605-4611; ; doi: 10.4049/jimmunol.177.7.4605 http://www.jimmunol.org/content/177/7/4605 Downloaded from References This article cites 39 articles, 16 of which you can access for free at: http://www.jimmunol.org/content/177/7/4605.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication by guest on September 23, 2021 *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2006 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Molecular Mechanisms for Transcriptional Regulation of Human High-Affinity IgE Receptor ␤-Chain Gene Induced by GM-CSF1 Kyoko Takahashi,*† Natsuko Hayashi,*‡ Shuichi Kaminogawa,† and Chisei Ra2* The ␤-chain of the high-affinity receptor for IgE (Fc␧RI) plays an important role in regulating activation of Fc␧RI-expressing cells such as mast cells in allergic reactions.
    [Show full text]
  • The Reaction Mechanism of Cellular U Snrnp Assembly
    The Reaction Mechanism of Cellular U snRNP Assembly Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Ashwin Chari Aus Bangalore (Indien) Würzburg 2009 Eingereicht am: Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. M. Müller 1. Gutachter: Prof. Dr. U. Fischer 2. Gutachter: Prof. Dr. U. Scheer Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am: Erklärung Erklärung gemäss §4 Absatz 3 der Promotionsordnung der Fakultät für Biologie der Bayerischen Julius-Maximilians-Universität Würzburg vom 15. März 1999 1. Hiermit erkläre ich ehrenwörtlich, dass ich die vorliegende Dissertation selbstständig angefertigt und keine anderen als die angegebenen Quellen und Hilfsmittel benutzt habe. 2. Ich erkläre, dass die vorliegende Dissertation weder in gleicher noch in ähnlicher Form bereits in einem Prüfungsverfahren vorgelegen hat. 3. Ich erkläre, dass ich ausser den mit dem Zulassungsantrag urkundlich vorgelegten Graden keine weiteren akademischen Grade erworben oder zu erwerben versucht habe. Würzburg, 2009 Ashwin Chari Table of Contents 1. Summary 1 2. Zusammenfassung 5 3. Introduction 9 3.1 Principles Governing Macromolecular Complex Assembly in Vivo 9 3.2 Pre-mRNA Splicing 12 3.3 Architecture of Spliceosomal U snRNPs 14 3.4 The Cell Biology of U snRNP Biogenesis 16 3.5 U snRNP Assembly in Vivo is an Active, Factor-Mediated Process 19 3.6 References 22 4. Goals of this Thesis 29 5. Results 31 5.1 Taking an Inventory of the Subunits of the Human SMN-Complex 31 5.2 Definition of the Basic Architecture of the Human SMN-Complex 49 5.3 Mechanistic Aspects of Cellular U snRNP Assembly 65 5.4 Evolution of the SMN-Complex 115 6.
    [Show full text]